Vladimir Putin was uncharacteristically fidgety as he spoke to supporters at the United Russia headquarters, as polls showed that voters had delivered a harsh blow to his party in parliamentary elections that were widely seen as a test of his personal popularity.

"I want to speak to all citizens of the country and, above all, those who voted for the party," Putin said, his eyebrows twitching and his gaze wandering. "Despite a rather complicated period in the life of our government, despite the [financial] crisis, despite the fact that responsibility for these difficulties has laid and lies on the shoulders of the party, people – our voters, our citizens – kept us as the leading political party in the country."

It was hardly the blustering rallying cry for which Putin has become known.

The vote on Sunday delivered the first concrete sign of Russians' unhappiness with Putin's announcement that he would seek re-election to the presidency in March. With 96% of the votes counted on Monday, United Russia's support stood at just under 50% – a sharp drop from the 64% it received in elections four years ago.

Observers are now anxiously watching how the former KGB agent will react.

"On the one hand, there's the option of moving towards the style of [Belarussian dictator Alexander] Lukashenko," said Alexei Navalny, an anti-corruption activist who rallied a web-based movement to get people to vote for any party but United Russia. "On the other, they realise that the harsher they are, the worse the result."

As the Kremlin prepares for the presidential vote, analysts say it will face a force it hasn't had to reckon with for over a decade – a politically conscious public.

"Groups of society have emerged that have a lively and serious interest in the vote results," said the political activist Gleb Pavlovsky. "They consider the results their own and that's why they are fighting for it."

The Kremlin has already taken note. Thousands of activists from Nashi, the Kremlin youth group, were bussed into the capital this weekend before a series of opposition protests. Nashi activists were already gathering at a site in central Moscow, where Solidarity, an umbrella opposition group, was due to hold a protest at 7pm (1500 GMT).

"I don't know that it will change anything," said Navalny, who supported the protest. "We cannot recognise these elections," he said, calling the widespread falsifications reported "nothing short of a crime". Observers from the Organisation for Security and Co-operation in Europe said the elections were marred by "frequent procedural violations and instances of apparent manipulations, including serious indications of ballot box stuffing".

"These elections were like a game in which only some players are allowed on the pitch, and then the field is tilted in favour of one of the players," Heidi Tagliavini, the head of the international observer mission, said.

The US secretary of state, Hillary Clinton, said the US had "serious concerns" about the conduct of the elections. "Russian voters deserve a full investigation of all credible reports of electoral fraud and manipulation and we hope in particular that then Russian authorities will take action," she said.

Russians continued to register alleged cases of falsification on Monday, and news reports on state television appeared to show results that implied turnout in some regions was as high as 146%.

Analysts do not expect to see a repeat of the scale of falsifications reported in Sunday's vote when Russians go to the polls in March. Putin's victory is widely expected – no serious opposition candidate has been allowed to emerge – so it was the parliamentary election that gave voters the chance to make their opinions known.

"It is clear that Putin's voter base has fallen apart," said Pavlovsky. "The Putin majority existed from 1999 to 2011 – this is the date of the end.

"I'm sure it was an unexpected surprise. He was sure voters would be enamoured of his return," he said. Instead, Putin has been met with boos at public events and an election result that, even with the alleged high level of falsifications, gives him the support of less than half the population. Voter turnout stood at around 60%.

United Russia scrambled to address the sharp drop in its support, which analysts put down to voters' concerns over the authoritarianism, ingrained corruption and falling living standards that Putin has presided over. Sergei Neverov, a top party official, was forced to deny rumours that Boris Gryzlov, the party chairman and speaker of the Duma, would resign following the result.

"We are quite satisfied with the speaker we currently have," Neverov said. "Today we can confidently say that the United Russia party received the moral right to continue the course of President Dmitry Medvedev and Prime Minister Vladimir Putin."

Another party official sought to put to rest worries that the result could put Putin's victory in the presidential vote in doubt. "As soon as we lose our confidence, we have nothing to do," Andrei Vorobyov, the chairman of the party's central executive committee, said.

"These 10 years [that Putin has been in power], it is very easy to lose confidence, but today it is at a very high level," he said. "Our candidate is known. It is Putin, our leader, and we will do everything in our power to ensure that our candidate wins in the first round."

Though Putin's popularity rating has dropped from the sky-high levels he regularly enjoyed after first coming to power in 1999, they still remain higher than any other politician in the country, coming in at around 50%, according to most pollsters.